Postdoctoral Researcher - Hamad Bin Khalifa University - Doha, Qatar
(2022-05)
Professor Omar Albagha Team | College of Health and Life Sciences
- Bioinformatics analyses; Manage whole genome sequencing data files in Unix/Linux HPC environment; employ shell and bash scripting to process, analyze, filter, annotate large data files. Merge, integrate phenotypic and genomic data.
- Population genetics and statistical epidemiology; running GWAS and heritability analyses for genome data collected from local individuals for multiple complex traits.
- Design, optimize and test polygenic risk scores for the datasets. Create linear and logistic regression statistical models to predict the phenotypes using PRS and further use adjusted R2 and AUROC to assess predictive capabilities of the PRS.
- Identify and assess quality control problems in data processing and analysis.
- Student mentorship and trainings: Support research students in their thesis projects and train them to use the software and tools required for data analysis.
- Manuscript preparation; Write and contribute to multiple publications for the team and for project collaborations.
Graduate (PhD) Student Researcher - Sidra Medicine - Doha, Qatar
(2018-08 - 2021-12)
Bioinformatics division | Pediatric Endocrinology Clinic. Understanding the genetics mechanisms underlying extreme short stature.
- Arranged and conducted patient recruitment, prepared registry and patient case assessment.
- Lab based: Blood processing, DNA extractions, functional studies
- Bioinformatics: Variant annotation, filtration, novel variant analysis
Graduate (Masters) Student Researcher - Imperial College of Science, Technology & Medicine - London, United Kingdom
(2017-03 - 2017-10)
Department of Surgery & Cancer. Metabolic phenotyping & immunometabolism in patients with acute & chronic liver disease
- Analyzed eicosanoid targeted UPLC/MS data using MassLynx/TargetLynx programs
- Employed statistical methods using SIMCA for data modeling.
- Worked with clinicians to integrate data modeling with patient clinical meta-data
Graduate (Masters) Student Researcher - Queen Mary University - London, United Kingdom
(2016-11 - 2017-03)
Department of Dentistry | Blizard Institute. Gut-derived microbial methylamines and short chain fatty acid metabolites', in vitro effect on blood-brain barrier function in a metabolites-specific manner
- Screened gut-derived microbial metabolites on hCMEC/D3 blood brain barrier (BBB) cell line; Carried out in vitro biochemical assays to determine impact of circulating metabolites upon efflux transporters; Cultured human endothelial cells and used flow cytometry techniques, qt-PCR, microarray data analysis
- Study was conducted to assess of metabolites effect on BBB that could be contributing to Alzheimer's disease.
Undergraduate Student Researcher - Carnegie Mellon University Qatar - Doha, Qatar
(2014-07 - 2016-05)
Biological Sciences Department. Sand bacteriophages and microbial composition genome analysis in Qatar | Senior Thesis Project
- Studied the use of bacteriophages as an alternative to antibiotics to overcome the growing problem of antimicrobial resistance.
- Collected samples from the environment (sand) to identify bacteriophages suitable for targeting the bacteria species Mycobacterium smegmatis, a less virulent family member of the species Mycobacterium tuberculosis.
- The SEA-PHAGES phage-hunting protocol was used which consisted of microbiology culturing techniques to grow bacteria and isolate, harvest and purify phages. Isolated High-purity DNA from purified phages and sequenced bacteriophage DNA using NGS
- Computational analyzed the genome of the isolated phages to identify the anti-bacterial elements as well as the genes conferring other beneficial properties.
- Used programs such as BLAST, SOAPDenovo, Velvet gene analysis programs working in a Unix/Linux environment.
Undergraduate Student Researcher - Carnegie Mellon University - Pittsburgh, USA
(2015-06 - 2015-08)
Hiller Lab | Mellon Institute. Quorum sensing in PMEN1 s. pneumoniae strains
- Biosafety Lab- Level 2, designed experiments using mutant and wild type strains to find a phenotype applicable to the stressed conditions of growth (with varying concentrations of hydrogen peroxide and paraquat).
- These experiments were done to better understand the quorum sensing systems in PMEN1 s.pneumoniae strains in an attempt to tackle infection and antibiotic resistance in this bacterial species; Participated in biological (safety) training as well as helped to mentor another student
